http://www.loni.ucla.edu/twiki/bin/view/CCB/PipelineWorkflows_BioinfoMAQ
http://maq.sourceforge.net/maq-man.shtml#use
pipeline://pws.loni.ucla.edu//ifs/tmp/pipelineTraining/{$username}/MAQ/results
pipeline://pws.loni.ucla.edu//ifs/tmp/pipelineTraining/{$username}/SAMtools/results
http://maq.sourceforge.net/maq-man.shtml#use
pipeline://pws.loni.ucla.edu//ifs/ccb/CCB_SW_Tools/BioinformaticsGenetics/test_data_2011/UCI_data_2011/test_pipeline/s_1_1_sequence.txt
pipeline://pws.loni.ucla.edu//ifs/ccb/CCB_SW_Tools/BioinformaticsGenetics/test_data_2011/UCI_data_2011/test_pipeline/s_1_2_sequence.txt
http://www.loni.ucla.edu
1
http://www.loni.ucla.edu
1000
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/
pipeline://pws.loni.ucla.edu//ifs/ccb/CCB_SW_Tools/BioinformaticsGenetics/MAQ_BWA_2010/test_data/ref_chr2.fasta
http://maq.sourceforge.net/maq-man.shtml#use
fastq2bfq
http://maq.sourceforge.net/maq-man.shtml#use
fasta2bfa
http://maq.sourceforge.net/maq-man.shtml#use
map
http://maq.sourceforge.net/maq-man.shtml#use
sol2sanger
http://samtools.sourceforge.net/samtools.shtml
sort
http://samtools.sourceforge.net/samtools.shtml
rmdup
http://samtools.sourceforge.net/samtools.shtml
-sS
http://samtools.sourceforge.net/samtools.shtml
calmd
http://samtools.sourceforge.net/samtools.shtml
index
http://samtools.sourceforge.net/samtools.shtml
faidx
http://samtools.sourceforge.net/samtools.shtml
-b
http://samtools.sourceforge.net/samtools.shtml
view
http://samtools.sourceforge.net/samtools.shtml
-bht
PMID: 2181060
PMID: 18714091
http://maq.sourceforge.net/maq-manpage.shtml#12
GPL
bioinformatics genomics
http://maq.sourceforge.net/maq-man.shtml
PMID: 2181060
PMID: 18714091
http://maq.sourceforge.net/maq-manpage.shtml#12
GPL
bioinformatics genomics
http://maq.sourceforge.net/maq-man.shtml
PMID: 2181060
PMID: 18714091
http://maq.sourceforge.net/maq-manpage.shtml#12
GPL
bioinformatics genomics
http://maq.sourceforge.net/maq-man.shtml
PMID: 2181060
PMID: 18714091
http://maq.sourceforge.net/maq-manpage.shtml#12
GPL
bioinformatics genomics
http://maq.sourceforge.net/maq-man.shtml
PMID: 19261174
PMID: 19930550
PMID: 19289445
http://www.cbcb.umd.edu/research/SR-assembly.shtml
open-source Artistic License
bioinformatics genomics
http://bowtie-bio.sourceforge.net/
-S
PMID: 19261174
PMID: 19930550
PMID: 19289445
http://www.cbcb.umd.edu/research/SR-assembly.shtml
open-source Artistic License
bioinformatics genomics
http://bowtie-bio.sourceforge.net/
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
.bam:.bam
PMID: 19505943
http://sourceforge.net/projects/samtools/
BSD
bioinformatics genomics
http://sourceforge.net/projects/samtools/
pipeline://pws.loni.ucla.edu//ifs/tmp/pipelineTraining/{$username}/Bowtie/results